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<h4>File: <a href="../master_function_v4.c" target="rtwreport_document_frame" id="linkToText_plain">master_function_v4.c</a></h4>
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<a name="1"><font color="#888888 "><i>    1   </i></font></a><font color="#117755"><i>/*</i></font>
<a name="2"><font color="#888888 "><i>    2   </i></font></a><font color="#117755"><I> * master_function_v4.c</i></font>
<a name="3"><font color="#888888 "><i>    3   </i></font></a><font color="#117755"><I> *</i></font>
<a name="4"><font color="#888888 "><i>    4   </i></font></a><font color="#117755"><I> * Code generation for function 'master_function_v4'</i></font>
<a name="5"><font color="#888888 "><i>    5   </i></font></a><font color="#117755"><I> *</i></font>
<a name="6"><font color="#888888 "><i>    6   </i></font></a><font color="#117755"><I> */</i></font>
<a name="7"><font color="#888888 "><i>    7   </i></font></a>
<a name="8"><font color="#888888 "><i>    8   </i></font></a><font color="#117755"><i>/* Include files */</i></font>
<a name="9"><font color="#888888 "><i>    9   </i></font></a><font color="#992211">#</font><font color="#992211"><b>include</b></font> <font color="#992211">&quot;rt_nonfinite.h&quot;</font>
<a name="10"><font color="#888888 "><i>   10   </i></font></a><font color="#992211">#</font><font color="#992211"><b>include</b></font> <font color="#992211">&quot;master_function_v4.h&quot;</font>
<a name="11"><font color="#888888 "><i>   11   </i></font></a><font color="#992211">#</font><font color="#992211"><b>include</b></font> <font color="#992211">&quot;sum.h&quot;</font>
<a name="12"><font color="#888888 "><i>   12   </i></font></a><font color="#992211">#</font><font color="#992211"><b>include</b></font> <font color="#992211">&quot;master_function_v4_mexutil.h&quot;</font>
<a name="13"><font color="#888888 "><i>   13   </i></font></a><font color="#992211">#</font><font color="#992211"><b>include</b></font> <font color="#992211">&quot;master_function_v4_data.h&quot;</font>
<a name="14"><font color="#888888 "><i>   14   </i></font></a>
<a name="15"><font color="#888888 "><i>   15   </i></font></a><font color="#117755"><i>/* Variable Definitions */</i></font>
<a name="16"><font color="#888888 "><i>   16   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_emlrtRSI">emlrtRSI</a> = <b>{</b> 9, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="17"><font color="#888888 "><i>   17   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>
<a name="18"><font color="#888888 "><i>   18   </i></font></a><b>}</b>;
<a name="19"><font color="#888888 "><i>   19   </i></font></a>
<a name="20"><font color="#888888 "><i>   20   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_b_emlrtRSI">b_emlrtRSI</a> = <b>{</b> 10, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="21"><font color="#888888 "><i>   21   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>
<a name="22"><font color="#888888 "><i>   22   </i></font></a><b>}</b>;
<a name="23"><font color="#888888 "><i>   23   </i></font></a>
<a name="24"><font color="#888888 "><i>   24   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_c_emlrtRSI">c_emlrtRSI</a> = <b>{</b> 16, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="25"><font color="#888888 "><i>   25   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>
<a name="26"><font color="#888888 "><i>   26   </i></font></a><b>}</b>;
<a name="27"><font color="#888888 "><i>   27   </i></font></a>
<a name="28"><font color="#888888 "><i>   28   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_d_emlrtRSI">d_emlrtRSI</a> = <b>{</b> 17, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="29"><font color="#888888 "><i>   29   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>
<a name="30"><font color="#888888 "><i>   30   </i></font></a><b>}</b>;
<a name="31"><font color="#888888 "><i>   31   </i></font></a>
<a name="32"><font color="#888888 "><i>   32   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_e_emlrtRSI">e_emlrtRSI</a> = <b>{</b> 34, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="33"><font color="#888888 "><i>   33   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>
<a name="34"><font color="#888888 "><i>   34   </i></font></a><b>}</b>;
<a name="35"><font color="#888888 "><i>   35   </i></font></a>
<a name="36"><font color="#888888 "><i>   36   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_f_emlrtRSI">f_emlrtRSI</a> = <b>{</b> 40, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="37"><font color="#888888 "><i>   37   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>
<a name="38"><font color="#888888 "><i>   38   </i></font></a><b>}</b>;
<a name="39"><font color="#888888 "><i>   39   </i></font></a>
<a name="40"><font color="#888888 "><i>   40   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_g_emlrtRSI">g_emlrtRSI</a> = <b>{</b> 41, <font color="#1122ff">&quot;find&quot;</font>,
<a name="41"><font color="#888888 "><i>   41   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\elmat\\find.m&quot;</font>
<a name="42"><font color="#888888 "><i>   42   </i></font></a><b>}</b>;
<a name="43"><font color="#888888 "><i>   43   </i></font></a>
<a name="44"><font color="#888888 "><i>   44   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_h_emlrtRSI">h_emlrtRSI</a> = <b>{</b> 68, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="45"><font color="#888888 "><i>   45   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="46"><font color="#888888 "><i>   46   </i></font></a><b>}</b>;
<a name="47"><font color="#888888 "><i>   47   </i></font></a>
<a name="48"><font color="#888888 "><i>   48   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_i_emlrtRSI">i_emlrtRSI</a> = <b>{</b> 21, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="49"><font color="#888888 "><i>   49   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="50"><font color="#888888 "><i>   50   </i></font></a><b>}</b>;
<a name="51"><font color="#888888 "><i>   51   </i></font></a>
<a name="52"><font color="#888888 "><i>   52   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_j_emlrtRSI">j_emlrtRSI</a> = <b>{</b> 54, <font color="#1122ff">&quot;eml_xgemm&quot;</font>,
<a name="53"><font color="#888888 "><i>   53   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\eml\\blas\\eml_xgemm.m&quot;</font>
<a name="54"><font color="#888888 "><i>   54   </i></font></a><b>}</b>;
<a name="55"><font color="#888888 "><i>   55   </i></font></a>
<a name="56"><font color="#888888 "><i>   56   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_k_emlrtRSI">k_emlrtRSI</a> = <b>{</b> 1, <font color="#1122ff">&quot;xgemm&quot;</font>,
<a name="57"><font color="#888888 "><i>   57   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\coder\\coder\\+coder\\+internal\\+blas\\xgemm.p&quot;</font>
<a name="58"><font color="#888888 "><i>   58   </i></font></a><b>}</b>;
<a name="59"><font color="#888888 "><i>   59   </i></font></a>
<a name="60"><font color="#888888 "><i>   60   </i></font></a><font color="#112266"><b>static</b></font> emlrtMCInfo <a name="var_emlrtMCI">emlrtMCI</a> = <b>{</b> 239, 9, <font color="#1122ff">&quot;find&quot;</font>,
<a name="61"><font color="#888888 "><i>   61   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\elmat\\find.m&quot;</font>
<a name="62"><font color="#888888 "><i>   62   </i></font></a><b>}</b>;
<a name="63"><font color="#888888 "><i>   63   </i></font></a>
<a name="64"><font color="#888888 "><i>   64   </i></font></a><font color="#112266"><b>static</b></font> emlrtMCInfo <a name="var_f_emlrtMCI">f_emlrtMCI</a> = <b>{</b> 99, 13, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="65"><font color="#888888 "><i>   65   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="66"><font color="#888888 "><i>   66   </i></font></a><b>}</b>;
<a name="67"><font color="#888888 "><i>   67   </i></font></a>
<a name="68"><font color="#888888 "><i>   68   </i></font></a><font color="#112266"><b>static</b></font> emlrtMCInfo <a name="var_g_emlrtMCI">g_emlrtMCI</a> = <b>{</b> 98, 23, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="69"><font color="#888888 "><i>   69   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="70"><font color="#888888 "><i>   70   </i></font></a><b>}</b>;
<a name="71"><font color="#888888 "><i>   71   </i></font></a>
<a name="72"><font color="#888888 "><i>   72   </i></font></a><font color="#112266"><b>static</b></font> emlrtMCInfo <a name="var_h_emlrtMCI">h_emlrtMCI</a> = <b>{</b> 104, 13, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="73"><font color="#888888 "><i>   73   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="74"><font color="#888888 "><i>   74   </i></font></a><b>}</b>;
<a name="75"><font color="#888888 "><i>   75   </i></font></a>
<a name="76"><font color="#888888 "><i>   76   </i></font></a><font color="#112266"><b>static</b></font> emlrtMCInfo <a name="var_i_emlrtMCI">i_emlrtMCI</a> = <b>{</b> 103, 23, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="77"><font color="#888888 "><i>   77   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="78"><font color="#888888 "><i>   78   </i></font></a><b>}</b>;
<a name="79"><font color="#888888 "><i>   79   </i></font></a>
<a name="80"><font color="#888888 "><i>   80   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_emlrtBCI">emlrtBCI</a> = <b>{</b> -1, -1, 1, 1, <font color="#1122ff">&quot;&quot;</font>, <font color="#1122ff">&quot;xgemm&quot;</font>,
<a name="81"><font color="#888888 "><i>   81   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\coder\\coder\\+coder\\+internal\\+blas\\xgemm.p&quot;</font>,
<a name="82"><font color="#888888 "><i>   82   </i></font></a>  0 <b>}</b>;
<a name="83"><font color="#888888 "><i>   83   </i></font></a>
<a name="84"><font color="#888888 "><i>   84   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_b_emlrtBCI">b_emlrtBCI</a> = <b>{</b> -1, -1, 24, 63, <font color="#1122ff">&quot;x_0&quot;</font>, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="85"><font color="#888888 "><i>   85   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="86"><font color="#888888 "><i>   86   </i></font></a>  0 <b>}</b>;
<a name="87"><font color="#888888 "><i>   87   </i></font></a>
<a name="88"><font color="#888888 "><i>   88   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_c_emlrtBCI">c_emlrtBCI</a> = <b>{</b> -1, -1, 24, 37, <font color="#1122ff">&quot;k_0&quot;</font>, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="89"><font color="#888888 "><i>   89   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="90"><font color="#888888 "><i>   90   </i></font></a>  0 <b>}</b>;
<a name="91"><font color="#888888 "><i>   91   </i></font></a>
<a name="92"><font color="#888888 "><i>   92   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_d_emlrtBCI">d_emlrtBCI</a> = <b>{</b> -1, -1, 37, 21, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="93"><font color="#888888 "><i>   93   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="94"><font color="#888888 "><i>   94   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="95"><font color="#888888 "><i>   95   </i></font></a>  0 <b>}</b>;
<a name="96"><font color="#888888 "><i>   96   </i></font></a>
<a name="97"><font color="#888888 "><i>   97   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_e_emlrtBCI">e_emlrtBCI</a> = <b>{</b> -1, -1, 37, 24, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="98"><font color="#888888 "><i>   98   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="99"><font color="#888888 "><i>   99   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="100"><font color="#888888 "><i>  100   </i></font></a>  0 <b>}</b>;
<a name="101"><font color="#888888 "><i>  101   </i></font></a>
<a name="102"><font color="#888888 "><i>  102   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_f_emlrtBCI">f_emlrtBCI</a> = <b>{</b> -1, -1, 37, 29, <font color="#1122ff">&quot;diagonal&quot;</font>,
<a name="103"><font color="#888888 "><i>  103   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="104"><font color="#888888 "><i>  104   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="105"><font color="#888888 "><i>  105   </i></font></a>  0 <b>}</b>;
<a name="106"><font color="#888888 "><i>  106   </i></font></a>
<a name="107"><font color="#888888 "><i>  107   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_g_emlrtBCI">g_emlrtBCI</a> = <b>{</b> -1, -1, 8, 35, <font color="#1122ff">&quot;transitions_matrix&quot;</font>,
<a name="108"><font color="#888888 "><i>  108   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="109"><font color="#888888 "><i>  109   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="110"><font color="#888888 "><i>  110   </i></font></a>  0 <b>}</b>;
<a name="111"><font color="#888888 "><i>  111   </i></font></a>
<a name="112"><font color="#888888 "><i>  112   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_h_emlrtBCI">h_emlrtBCI</a> = <b>{</b> -1, -1, 8, 38, <font color="#1122ff">&quot;transitions_matrix&quot;</font>,
<a name="113"><font color="#888888 "><i>  113   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="114"><font color="#888888 "><i>  114   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="115"><font color="#888888 "><i>  115   </i></font></a>  0 <b>}</b>;
<a name="116"><font color="#888888 "><i>  116   </i></font></a>
<a name="117"><font color="#888888 "><i>  117   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_i_emlrtBCI">i_emlrtBCI</a> = <b>{</b> -1, -1, 13, 27, <font color="#1122ff">&quot;initial_rates&quot;</font>,
<a name="118"><font color="#888888 "><i>  118   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="119"><font color="#888888 "><i>  119   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="120"><font color="#888888 "><i>  120   </i></font></a>  0 <b>}</b>;
<a name="121"><font color="#888888 "><i>  121   </i></font></a>
<a name="122"><font color="#888888 "><i>  122   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_j_emlrtBCI">j_emlrtBCI</a> = <b>{</b> -1, -1, 11, 27, <font color="#1122ff">&quot;x&quot;</font>, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="123"><font color="#888888 "><i>  123   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="124"><font color="#888888 "><i>  124   </i></font></a>  0 <b>}</b>;
<a name="125"><font color="#888888 "><i>  125   </i></font></a>
<a name="126"><font color="#888888 "><i>  126   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_k_emlrtBCI">k_emlrtBCI</a> = <b>{</b> -1, -1, 20, 27, <font color="#1122ff">&quot;initial_rates&quot;</font>,
<a name="127"><font color="#888888 "><i>  127   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="128"><font color="#888888 "><i>  128   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="129"><font color="#888888 "><i>  129   </i></font></a>  0 <b>}</b>;
<a name="130"><font color="#888888 "><i>  130   </i></font></a>
<a name="131"><font color="#888888 "><i>  131   </i></font></a><font color="#112266"><b>static</b></font> emlrtDCInfo <a name="var_emlrtDCI">emlrtDCI</a> = <b>{</b> 20, 27, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="132"><font color="#888888 "><i>  132   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="133"><font color="#888888 "><i>  133   </i></font></a>  1 <b>}</b>;
<a name="134"><font color="#888888 "><i>  134   </i></font></a>
<a name="135"><font color="#888888 "><i>  135   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_l_emlrtBCI">l_emlrtBCI</a> = <b>{</b> -1, -1, 18, 27, <font color="#1122ff">&quot;x&quot;</font>, <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="136"><font color="#888888 "><i>  136   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="137"><font color="#888888 "><i>  137   </i></font></a>  0 <b>}</b>;
<a name="138"><font color="#888888 "><i>  138   </i></font></a>
<a name="139"><font color="#888888 "><i>  139   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_m_emlrtBCI">m_emlrtBCI</a> = <b>{</b> -1, -1, 24, 29, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="140"><font color="#888888 "><i>  140   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="141"><font color="#888888 "><i>  141   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="142"><font color="#888888 "><i>  142   </i></font></a>  0 <b>}</b>;
<a name="143"><font color="#888888 "><i>  143   </i></font></a>
<a name="144"><font color="#888888 "><i>  144   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_n_emlrtBCI">n_emlrtBCI</a> = <b>{</b> -1, -1, 24, 32, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="145"><font color="#888888 "><i>  145   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="146"><font color="#888888 "><i>  146   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="147"><font color="#888888 "><i>  147   </i></font></a>  0 <b>}</b>;
<a name="148"><font color="#888888 "><i>  148   </i></font></a>
<a name="149"><font color="#888888 "><i>  149   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_o_emlrtBCI">o_emlrtBCI</a> = <b>{</b> -1, -1, 26, 32, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="150"><font color="#888888 "><i>  150   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="151"><font color="#888888 "><i>  151   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="152"><font color="#888888 "><i>  152   </i></font></a>  0 <b>}</b>;
<a name="153"><font color="#888888 "><i>  153   </i></font></a>
<a name="154"><font color="#888888 "><i>  154   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_p_emlrtBCI">p_emlrtBCI</a> = <b>{</b> -1, -1, 26, 35, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="155"><font color="#888888 "><i>  155   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="156"><font color="#888888 "><i>  156   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="157"><font color="#888888 "><i>  157   </i></font></a>  0 <b>}</b>;
<a name="158"><font color="#888888 "><i>  158   </i></font></a>
<a name="159"><font color="#888888 "><i>  159   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_q_emlrtBCI">q_emlrtBCI</a> = <b>{</b> -1, -1, 27, 33, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="160"><font color="#888888 "><i>  160   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="161"><font color="#888888 "><i>  161   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="162"><font color="#888888 "><i>  162   </i></font></a>  0 <b>}</b>;
<a name="163"><font color="#888888 "><i>  163   </i></font></a>
<a name="164"><font color="#888888 "><i>  164   </i></font></a><font color="#112266"><b>static</b></font> emlrtBCInfo <a name="var_r_emlrtBCI">r_emlrtBCI</a> = <b>{</b> -1, -1, 27, 36, <font color="#1122ff">&quot;rate_matrix&quot;</font>,
<a name="165"><font color="#888888 "><i>  165   </i></font></a>  <font color="#1122ff">&quot;master_function_v4&quot;</font>,
<a name="166"><font color="#888888 "><i>  166   </i></font></a>  <font color="#1122ff">&quot;G:\\Mingxi\\Dropbox\\Thesis Proposal\\codes\\trunk\\parameterfiting\\master_function_v4.m&quot;</font>,
<a name="167"><font color="#888888 "><i>  167   </i></font></a>  0 <b>}</b>;
<a name="168"><font color="#888888 "><i>  168   </i></font></a>
<a name="169"><font color="#888888 "><i>  169   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_n_emlrtRSI">n_emlrtRSI</a> = <b>{</b> 239, <font color="#1122ff">&quot;find&quot;</font>,
<a name="170"><font color="#888888 "><i>  170   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\elmat\\find.m&quot;</font>
<a name="171"><font color="#888888 "><i>  171   </i></font></a><b>}</b>;
<a name="172"><font color="#888888 "><i>  172   </i></font></a>
<a name="173"><font color="#888888 "><i>  173   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_o_emlrtRSI">o_emlrtRSI</a> = <b>{</b> 98, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="174"><font color="#888888 "><i>  174   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="175"><font color="#888888 "><i>  175   </i></font></a><b>}</b>;
<a name="176"><font color="#888888 "><i>  176   </i></font></a>
<a name="177"><font color="#888888 "><i>  177   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_p_emlrtRSI">p_emlrtRSI</a> = <b>{</b> 103, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="178"><font color="#888888 "><i>  178   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="179"><font color="#888888 "><i>  179   </i></font></a><b>}</b>;
<a name="180"><font color="#888888 "><i>  180   </i></font></a>
<a name="181"><font color="#888888 "><i>  181   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_s_emlrtRSI">s_emlrtRSI</a> = <b>{</b> 99, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="182"><font color="#888888 "><i>  182   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="183"><font color="#888888 "><i>  183   </i></font></a><b>}</b>;
<a name="184"><font color="#888888 "><i>  184   </i></font></a>
<a name="185"><font color="#888888 "><i>  185   </i></font></a><font color="#112266"><b>static</b></font> emlrtRSInfo <a name="var_t_emlrtRSI">t_emlrtRSI</a> = <b>{</b> 104, <font color="#1122ff">&quot;eml_mtimes_helper&quot;</font>,
<a name="186"><font color="#888888 "><i>  186   </i></font></a>  <font color="#1122ff">&quot;C:\\Program Files\\MATLAB\\R2014a\\toolbox\\eml\\lib\\matlab\\ops\\eml_mtimes_helper.m&quot;</font>
<a name="187"><font color="#888888 "><i>  187   </i></font></a><b>}</b>;
<a name="188"><font color="#888888 "><i>  188   </i></font></a>
<a name="189"><font color="#888888 "><i>  189   </i></font></a><font color="#117755"><i>/* Function Definitions */</i></font>
<a name="190"><font color="#888888 "><i>  190   </i></font></a><font color="#112266"><b>void</b></font> <a name="fcn_master_function_v4">master_function_v4</a>(<font color="#112266"><b>const</b></font> emlrtStack *sp, real_T t, <font color="#112266"><b>const</b></font> real_T y_data[],
<a name="191"><font color="#888888 "><i>  191   </i></font></a>  <font color="#112266"><b>const</b></font> int32_T y_size[1], <font color="#112266"><b>const</b></font> real_T x_data[], <font color="#112266"><b>const</b></font> int32_T x_size[2], <font color="#112266"><b>const</b></font>
<a name="192"><font color="#888888 "><i>  192   </i></font></a>  real_T transitions_matrix_data[], <font color="#112266"><b>const</b></font> int32_T transitions_matrix_size[2],
<a name="193"><font color="#888888 "><i>  193   </i></font></a>  real_T force_rate, <font color="#112266"><b>const</b></font> real_T variables_indexes_data[], <font color="#112266"><b>const</b></font> int32_T
<a name="194"><font color="#888888 "><i>  194   </i></font></a>  variables_indexes_size[2], <font color="#112266"><b>const</b></font> real_T initial_rates_data[], <font color="#112266"><b>const</b></font> int32_T
<a name="195"><font color="#888888 "><i>  195   </i></font></a>  initial_rates_size[2], real_T dy_data[], int32_T dy_size[1])
<a name="196"><font color="#888888 "><i>  196   </i></font></a><b>{</b>
<a name="197"><font color="#888888 "><i>  197   </i></font></a>  real_T s;
<a name="198"><font color="#888888 "><i>  198   </i></font></a>  real_T N;
<a name="199"><font color="#888888 "><i>  199   </i></font></a>  int32_T rate_matrix_size[2];
<a name="200"><font color="#888888 "><i>  200   </i></font></a>  int32_T ix;
<a name="201"><font color="#888888 "><i>  201   </i></font></a>  int32_T iy;
<a name="202"><font color="#888888 "><i>  202   </i></font></a>  real_T rate_matrix_data[100];
<a name="203"><font color="#888888 "><i>  203   </i></font></a>  int32_T n;
<a name="204"><font color="#888888 "><i>  204   </i></font></a>  int32_T i;
<a name="205"><font color="#888888 "><i>  205   </i></font></a>  int32_T b_n;
<a name="206"><font color="#888888 "><i>  206   </i></font></a>  int32_T j;
<a name="207"><font color="#888888 "><i>  207   </i></font></a>  boolean_T b_x_data[50];
<a name="208"><font color="#888888 "><i>  208   </i></font></a>  int32_T ixstart;
<a name="209"><font color="#888888 "><i>  209   </i></font></a>  int32_T ii_data[50];
<a name="210"><font color="#888888 "><i>  210   </i></font></a>  int32_T diagonal_size_idx_1;
<a name="211"><font color="#888888 "><i>  211   </i></font></a>  boolean_T exitg3;
<a name="212"><font color="#888888 "><i>  212   </i></font></a>  boolean_T guard2 = false;
<a name="213"><font color="#888888 "><i>  213   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *y;
<a name="214"><font color="#888888 "><i>  214   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *m0;
<a name="215"><font color="#888888 "><i>  215   </i></font></a>  int32_T b_ii_data[50];
<a name="216"><font color="#888888 "><i>  216   </i></font></a>  int32_T index_size[2];
<a name="217"><font color="#888888 "><i>  217   </i></font></a>  real_T index_data[50];
<a name="218"><font color="#888888 "><i>  218   </i></font></a>  int32_T k_0_size_idx_1;
<a name="219"><font color="#888888 "><i>  219   </i></font></a>  real_T k_0_data[50];
<a name="220"><font color="#888888 "><i>  220   </i></font></a>  real_T alpha1;
<a name="221"><font color="#888888 "><i>  221   </i></font></a>  boolean_T exitg2;
<a name="222"><font color="#888888 "><i>  222   </i></font></a>  boolean_T guard1 = false;
<a name="223"><font color="#888888 "><i>  223   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *b_y;
<a name="224"><font color="#888888 "><i>  224   </i></font></a>  real_T x_0_data[50];
<a name="225"><font color="#888888 "><i>  225   </i></font></a>  boolean_T p;
<a name="226"><font color="#888888 "><i>  226   </i></font></a>  boolean_T b_p;
<a name="227"><font color="#888888 "><i>  227   </i></font></a>  int32_T exitg1;
<a name="228"><font color="#888888 "><i>  228   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *c_y;
<a name="229"><font color="#888888 "><i>  229   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> int32_T iv0[2] = <b>{</b> 1, 30 <b>}</b>;
<a name="230"><font color="#888888 "><i>  230   </i></font></a>
<a name="231"><font color="#888888 "><i>  231   </i></font></a>  char_T cv0[30];
<a name="232"><font color="#888888 "><i>  232   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> char_T cv1[30] = <b>{</b> <font color="#1122ff">'C'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'d'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'r'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'o'</font>,
<a name="233"><font color="#888888 "><i>  233   </i></font></a>    <font color="#1122ff">'l'</font>, <font color="#1122ff">'b'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'x'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'s'</font>, <font color="#1122ff">'u'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'_'</font>, <font color="#1122ff">'s'</font>, <font color="#1122ff">'p'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'c'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'a'</font>,
<a name="234"><font color="#888888 "><i>  234   </i></font></a>    <font color="#1122ff">'l'</font>, <font color="#1122ff">'E'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'p'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'y'</font> <b>}</b>;
<a name="235"><font color="#888888 "><i>  235   </i></font></a>
<a name="236"><font color="#888888 "><i>  236   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *d_y;
<a name="237"><font color="#888888 "><i>  237   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> int32_T iv1[2] = <b>{</b> 1, 36 <b>}</b>;
<a name="238"><font color="#888888 "><i>  238   </i></font></a>
<a name="239"><font color="#888888 "><i>  239   </i></font></a>  char_T cv2[36];
<a name="240"><font color="#888888 "><i>  240   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> char_T cv3[36] = <b>{</b> <font color="#1122ff">'C'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'d'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'r'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'o'</font>,
<a name="241"><font color="#888888 "><i>  241   </i></font></a>    <font color="#1122ff">'l'</font>, <font color="#1122ff">'b'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'x'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'a'</font>, <font color="#1122ff">'u'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'D'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'I'</font>, <font color="#1122ff">'n'</font>, <font color="#1122ff">'c'</font>,
<a name="242"><font color="#888888 "><i>  242   </i></font></a>    <font color="#1122ff">'o'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'p'</font>, <font color="#1122ff">'a'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'b'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'l'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'y'</font> <b>}</b>;
<a name="243"><font color="#888888 "><i>  243   </i></font></a>
<a name="244"><font color="#888888 "><i>  244   </i></font></a>  int8_T sz[2];
<a name="245"><font color="#888888 "><i>  245   </i></font></a>  real_T diagonal_data[10];
<a name="246"><font color="#888888 "><i>  246   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *e_y;
<a name="247"><font color="#888888 "><i>  247   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> int32_T iv2[2] = <b>{</b> 1, 45 <b>}</b>;
<a name="248"><font color="#888888 "><i>  248   </i></font></a>
<a name="249"><font color="#888888 "><i>  249   </i></font></a>  char_T cv4[45];
<a name="250"><font color="#888888 "><i>  250   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> char_T cv5[45] = <b>{</b> <font color="#1122ff">'C'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'d'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'r'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'o'</font>,
<a name="251"><font color="#888888 "><i>  251   </i></font></a>    <font color="#1122ff">'l'</font>, <font color="#1122ff">'b'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'x'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'t'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'s'</font>, <font color="#1122ff">'_'</font>, <font color="#1122ff">'n'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'D'</font>,
<a name="252"><font color="#888888 "><i>  252   </i></font></a>    <font color="#1122ff">'y'</font>, <font color="#1122ff">'n'</font>, <font color="#1122ff">'a'</font>, <font color="#1122ff">'m'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'c'</font>, <font color="#1122ff">'S'</font>, <font color="#1122ff">'c'</font>, <font color="#1122ff">'a'</font>, <font color="#1122ff">'l'</font>, <font color="#1122ff">'a'</font>, <font color="#1122ff">'r'</font>, <font color="#1122ff">'E'</font>, <font color="#1122ff">'x'</font>, <font color="#1122ff">'p'</font>,
<a name="253"><font color="#888888 "><i>  253   </i></font></a>    <font color="#1122ff">'a'</font>, <font color="#1122ff">'n'</font>, <font color="#1122ff">'s'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'n'</font> <b>}</b>;
<a name="254"><font color="#888888 "><i>  254   </i></font></a>
<a name="255"><font color="#888888 "><i>  255   </i></font></a>  <font color="#112266"><b>const</b></font> mxArray *f_y;
<a name="256"><font color="#888888 "><i>  256   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> int32_T iv3[2] = <b>{</b> 1, 21 <b>}</b>;
<a name="257"><font color="#888888 "><i>  257   </i></font></a>
<a name="258"><font color="#888888 "><i>  258   </i></font></a>  char_T cv6[21];
<a name="259"><font color="#888888 "><i>  259   </i></font></a>  <font color="#112266"><b>static</b></font> <font color="#112266"><b>const</b></font> char_T cv7[21] = <b>{</b> <font color="#1122ff">'C'</font>, <font color="#1122ff">'o'</font>, <font color="#1122ff">'d'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'r'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'M'</font>, <font color="#1122ff">'A'</font>, <font color="#1122ff">'T'</font>,
<a name="260"><font color="#888888 "><i>  260   </i></font></a>    <font color="#1122ff">'L'</font>, <font color="#1122ff">'A'</font>, <font color="#1122ff">'B'</font>, <font color="#1122ff">':'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'n'</font>, <font color="#1122ff">'n'</font>, <font color="#1122ff">'e'</font>, <font color="#1122ff">'r'</font>, <font color="#1122ff">'d'</font>, <font color="#1122ff">'i'</font>, <font color="#1122ff">'m'</font> <b>}</b>;
<a name="261"><font color="#888888 "><i>  261   </i></font></a>
<a name="262"><font color="#888888 "><i>  262   </i></font></a>  char_T TRANSB;
<a name="263"><font color="#888888 "><i>  263   </i></font></a>  char_T TRANSA;
<a name="264"><font color="#888888 "><i>  264   </i></font></a>  ptrdiff_t m_t;
<a name="265"><font color="#888888 "><i>  265   </i></font></a>  ptrdiff_t n_t;
<a name="266"><font color="#888888 "><i>  266   </i></font></a>  ptrdiff_t k_t;
<a name="267"><font color="#888888 "><i>  267   </i></font></a>  ptrdiff_t lda_t;
<a name="268"><font color="#888888 "><i>  268   </i></font></a>  ptrdiff_t ldb_t;
<a name="269"><font color="#888888 "><i>  269   </i></font></a>  ptrdiff_t ldc_t;
<a name="270"><font color="#888888 "><i>  270   </i></font></a>  <font color="#112266"><b>double</b></font> * alpha1_t;
<a name="271"><font color="#888888 "><i>  271   </i></font></a>  <font color="#112266"><b>double</b></font> * Aia0_t;
<a name="272"><font color="#888888 "><i>  272   </i></font></a>  <font color="#112266"><b>double</b></font> * Bib0_t;
<a name="273"><font color="#888888 "><i>  273   </i></font></a>  <font color="#112266"><b>double</b></font> * beta1_t;
<a name="274"><font color="#888888 "><i>  274   </i></font></a>  <font color="#112266"><b>double</b></font> * Cic0_t;
<a name="275"><font color="#888888 "><i>  275   </i></font></a>  emlrtStack st;
<a name="276"><font color="#888888 "><i>  276   </i></font></a>  emlrtStack b_st;
<a name="277"><font color="#888888 "><i>  277   </i></font></a>  emlrtStack c_st;
<a name="278"><font color="#888888 "><i>  278   </i></font></a>  emlrtStack d_st;
<a name="279"><font color="#888888 "><i>  279   </i></font></a>  emlrtStack e_st;
<a name="280"><font color="#888888 "><i>  280   </i></font></a>  emlrtStack f_st;
<a name="281"><font color="#888888 "><i>  281   </i></font></a>  st.prev = sp;
<a name="282"><font color="#888888 "><i>  282   </i></font></a>  st.tls = sp-&gt;tls;
<a name="283"><font color="#888888 "><i>  283   </i></font></a>  b_st.prev = &amp;st;
<a name="284"><font color="#888888 "><i>  284   </i></font></a>  b_st.tls = st.tls;
<a name="285"><font color="#888888 "><i>  285   </i></font></a>  c_st.prev = &amp;st;
<a name="286"><font color="#888888 "><i>  286   </i></font></a>  c_st.tls = st.tls;
<a name="287"><font color="#888888 "><i>  287   </i></font></a>  d_st.prev = &amp;b_st;
<a name="288"><font color="#888888 "><i>  288   </i></font></a>  d_st.tls = b_st.tls;
<a name="289"><font color="#888888 "><i>  289   </i></font></a>  e_st.prev = &amp;b_st;
<a name="290"><font color="#888888 "><i>  290   </i></font></a>  e_st.tls = b_st.tls;
<a name="291"><font color="#888888 "><i>  291   </i></font></a>  f_st.prev = &amp;d_st;
<a name="292"><font color="#888888 "><i>  292   </i></font></a>  f_st.tls = d_st.tls;
<a name="293"><font color="#888888 "><i>  293   </i></font></a>  s = 1.0;
<a name="294"><font color="#888888 "><i>  294   </i></font></a>  N = (real_T)initial_rates_size[1] / 2.0;
<a name="295"><font color="#888888 "><i>  295   </i></font></a>  rate_matrix_size[0] = transitions_matrix_size[0];
<a name="296"><font color="#888888 "><i>  296   </i></font></a>  rate_matrix_size[1] = transitions_matrix_size[1];
<a name="297"><font color="#888888 "><i>  297   </i></font></a>  ix = transitions_matrix_size[0] * transitions_matrix_size[1];
<a name="298"><font color="#888888 "><i>  298   </i></font></a>  <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="299"><font color="#888888 "><i>  299   </i></font></a>    rate_matrix_data[iy] = transitions_matrix_data[iy];
<a name="300"><font color="#888888 "><i>  300   </i></font></a>  <b>}</b>
<a name="301"><font color="#888888 "><i>  301   </i></font></a>
<a name="302"><font color="#888888 "><i>  302   </i></font></a>  <font color="#112266"><b>if</b></font> ((0 == transitions_matrix_size[0]) || (0 == transitions_matrix_size[1])) <b>{</b>
<a name="303"><font color="#888888 "><i>  303   </i></font></a>    n = 0;
<a name="304"><font color="#888888 "><i>  304   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="305"><font color="#888888 "><i>  305   </i></font></a>    n = muIntScalarMax_sint32(transitions_matrix_size[0],
<a name="306"><font color="#888888 "><i>  306   </i></font></a>      transitions_matrix_size[1]);
<a name="307"><font color="#888888 "><i>  307   </i></font></a>  <b>}</b>
<a name="308"><font color="#888888 "><i>  308   </i></font></a>
<a name="309"><font color="#888888 "><i>  309   </i></font></a>  i = 1;
<a name="310"><font color="#888888 "><i>  310   </i></font></a>  <font color="#112266"><b>while</b></font> (i - 1 &lt;= n - 1) <b>{</b>
<a name="311"><font color="#888888 "><i>  311   </i></font></a>    <font color="#112266"><b>if</b></font> ((0 == transitions_matrix_size[0]) || (0 == transitions_matrix_size[1]))
<a name="312"><font color="#888888 "><i>  312   </i></font></a>    <b>{</b>
<a name="313"><font color="#888888 "><i>  313   </i></font></a>      b_n = 0;
<a name="314"><font color="#888888 "><i>  314   </i></font></a>    <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="315"><font color="#888888 "><i>  315   </i></font></a>      b_n = muIntScalarMax_sint32(transitions_matrix_size[0],
<a name="316"><font color="#888888 "><i>  316   </i></font></a>        transitions_matrix_size[1]);
<a name="317"><font color="#888888 "><i>  317   </i></font></a>    <b>}</b>
<a name="318"><font color="#888888 "><i>  318   </i></font></a>
<a name="319"><font color="#888888 "><i>  319   </i></font></a>    j = 1;
<a name="320"><font color="#888888 "><i>  320   </i></font></a>    <font color="#112266"><b>while</b></font> (j - 1 &lt;= b_n - 1) <b>{</b>
<a name="321"><font color="#888888 "><i>  321   </i></font></a>      <font color="#112266"><b>if</b></font> (transitions_matrix_data[(emlrtDynamicBoundsCheckFastR2012b(i, 1,
<a name="322"><font color="#888888 "><i>  322   </i></font></a>            transitions_matrix_size[0], &amp;<a href="#var_g_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_g_emlrtBCI');" target="_self"><font color="#1122aa">g_emlrtBCI</font></a>, sp) +
<a name="323"><font color="#888888 "><i>  323   </i></font></a>           transitions_matrix_size[0] * (emlrtDynamicBoundsCheckFastR2012b(j, 1,
<a name="324"><font color="#888888 "><i>  324   </i></font></a>             transitions_matrix_size[1], &amp;<a href="#var_h_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_h_emlrtBCI');" target="_self"><font color="#1122aa">h_emlrtBCI</font></a>, sp) - 1)) - 1] &gt; 0.0) <b>{</b>
<a name="325"><font color="#888888 "><i>  325   </i></font></a>        st.site = &amp;<a href="#var_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtRSI');" target="_self"><font color="#1122aa">emlrtRSI</font></a>;
<a name="326"><font color="#888888 "><i>  326   </i></font></a>        ix = variables_indexes_size[0] * variables_indexes_size[1];
<a name="327"><font color="#888888 "><i>  327   </i></font></a>        <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="328"><font color="#888888 "><i>  328   </i></font></a>          b_x_data[iy] = (variables_indexes_data[iy] == s);
<a name="329"><font color="#888888 "><i>  329   </i></font></a>        <b>}</b>
<a name="330"><font color="#888888 "><i>  330   </i></font></a>
<a name="331"><font color="#888888 "><i>  331   </i></font></a>        b_st.site = &amp;<a href="#var_g_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_g_emlrtRSI');" target="_self"><font color="#1122aa">g_emlrtRSI</font></a>;
<a name="332"><font color="#888888 "><i>  332   </i></font></a>        ixstart = 0;
<a name="333"><font color="#888888 "><i>  333   </i></font></a>        diagonal_size_idx_1 = variables_indexes_size[1];
<a name="334"><font color="#888888 "><i>  334   </i></font></a>        ix = 1;
<a name="335"><font color="#888888 "><i>  335   </i></font></a>        exitg3 = false;
<a name="336"><font color="#888888 "><i>  336   </i></font></a>        <font color="#112266"><b>while</b></font> ((!exitg3) &amp;&amp; (ix &lt;= variables_indexes_size[1])) <b>{</b>
<a name="337"><font color="#888888 "><i>  337   </i></font></a>          guard2 = false;
<a name="338"><font color="#888888 "><i>  338   </i></font></a>          <font color="#112266"><b>if</b></font> (b_x_data[ix - 1]) <b>{</b>
<a name="339"><font color="#888888 "><i>  339   </i></font></a>            ixstart++;
<a name="340"><font color="#888888 "><i>  340   </i></font></a>            ii_data[ixstart - 1] = ix;
<a name="341"><font color="#888888 "><i>  341   </i></font></a>            <font color="#112266"><b>if</b></font> (ixstart &gt;= variables_indexes_size[1]) <b>{</b>
<a name="342"><font color="#888888 "><i>  342   </i></font></a>              exitg3 = true;
<a name="343"><font color="#888888 "><i>  343   </i></font></a>            <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="344"><font color="#888888 "><i>  344   </i></font></a>              guard2 = true;
<a name="345"><font color="#888888 "><i>  345   </i></font></a>            <b>}</b>
<a name="346"><font color="#888888 "><i>  346   </i></font></a>          <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="347"><font color="#888888 "><i>  347   </i></font></a>            guard2 = true;
<a name="348"><font color="#888888 "><i>  348   </i></font></a>          <b>}</b>
<a name="349"><font color="#888888 "><i>  349   </i></font></a>
<a name="350"><font color="#888888 "><i>  350   </i></font></a>          <font color="#112266"><b>if</b></font> (guard2) <b>{</b>
<a name="351"><font color="#888888 "><i>  351   </i></font></a>            ix++;
<a name="352"><font color="#888888 "><i>  352   </i></font></a>          <b>}</b>
<a name="353"><font color="#888888 "><i>  353   </i></font></a>        <b>}</b>
<a name="354"><font color="#888888 "><i>  354   </i></font></a>
<a name="355"><font color="#888888 "><i>  355   </i></font></a>        <font color="#112266"><b>if</b></font> (ixstart &lt;= variables_indexes_size[1]) <b>{</b>
<a name="356"><font color="#888888 "><i>  356   </i></font></a>        <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="357"><font color="#888888 "><i>  357   </i></font></a>          y = NULL;
<a name="358"><font color="#888888 "><i>  358   </i></font></a>          m0 = emlrtCreateString(<font color="#1122ff">&quot;Assertion failed.&quot;</font>);
<a name="359"><font color="#888888 "><i>  359   </i></font></a>          emlrtAssign(&amp;y, m0);
<a name="360"><font color="#888888 "><i>  360   </i></font></a>          d_st.site = &amp;<a href="#var_n_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_n_emlrtRSI');" target="_self"><font color="#1122aa">n_emlrtRSI</font></a>;
<a name="361"><font color="#888888 "><i>  361   </i></font></a>          <a href="master_function_v4_mexutil_c.html#fcn_error" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_error');" target="_self"><font color="#1122aa">error</font></a>(&amp;d_st, y, &amp;<a href="#var_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtMCI');" target="_self"><font color="#1122aa">emlrtMCI</font></a>);
<a name="362"><font color="#888888 "><i>  362   </i></font></a>        <b>}</b>
<a name="363"><font color="#888888 "><i>  363   </i></font></a>
<a name="364"><font color="#888888 "><i>  364   </i></font></a>        <font color="#112266"><b>if</b></font> (variables_indexes_size[1] == 1) <b>{</b>
<a name="365"><font color="#888888 "><i>  365   </i></font></a>          <font color="#112266"><b>if</b></font> (ixstart == 0) <b>{</b>
<a name="366"><font color="#888888 "><i>  366   </i></font></a>            diagonal_size_idx_1 = 0;
<a name="367"><font color="#888888 "><i>  367   </i></font></a>          <b>}</b>
<a name="368"><font color="#888888 "><i>  368   </i></font></a>        <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="369"><font color="#888888 "><i>  369   </i></font></a>          <font color="#112266"><b>if</b></font> (1 &gt; ixstart) <b>{</b>
<a name="370"><font color="#888888 "><i>  370   </i></font></a>            diagonal_size_idx_1 = 0;
<a name="371"><font color="#888888 "><i>  371   </i></font></a>          <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="372"><font color="#888888 "><i>  372   </i></font></a>            diagonal_size_idx_1 = ixstart;
<a name="373"><font color="#888888 "><i>  373   </i></font></a>          <b>}</b>
<a name="374"><font color="#888888 "><i>  374   </i></font></a>
<a name="375"><font color="#888888 "><i>  375   </i></font></a>          <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="376"><font color="#888888 "><i>  376   </i></font></a>            b_ii_data[iy] = ii_data[iy];
<a name="377"><font color="#888888 "><i>  377   </i></font></a>          <b>}</b>
<a name="378"><font color="#888888 "><i>  378   </i></font></a>
<a name="379"><font color="#888888 "><i>  379   </i></font></a>          <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="380"><font color="#888888 "><i>  380   </i></font></a>            ii_data[iy] = b_ii_data[iy];
<a name="381"><font color="#888888 "><i>  381   </i></font></a>          <b>}</b>
<a name="382"><font color="#888888 "><i>  382   </i></font></a>        <b>}</b>
<a name="383"><font color="#888888 "><i>  383   </i></font></a>
<a name="384"><font color="#888888 "><i>  384   </i></font></a>        index_size[0] = 1;
<a name="385"><font color="#888888 "><i>  385   </i></font></a>        index_size[1] = diagonal_size_idx_1;
<a name="386"><font color="#888888 "><i>  386   </i></font></a>        ix = diagonal_size_idx_1;
<a name="387"><font color="#888888 "><i>  387   </i></font></a>        <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="388"><font color="#888888 "><i>  388   </i></font></a>          index_data[iy] = ii_data[iy];
<a name="389"><font color="#888888 "><i>  389   </i></font></a>        <b>}</b>
<a name="390"><font color="#888888 "><i>  390   </i></font></a>
<a name="391"><font color="#888888 "><i>  391   </i></font></a>        st.site = &amp;<a href="#var_b_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_b_emlrtRSI');" target="_self"><font color="#1122aa">b_emlrtRSI</font></a>;
<a name="392"><font color="#888888 "><i>  392   </i></font></a>        <font color="#112266"><b>if</b></font> (<a href="sum_c.html#fcn_sum" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_sum');" target="_self"><font color="#1122aa">sum</font></a>(&amp;st, index_data, index_size) &gt; 0.0) <b>{</b>
<a name="393"><font color="#888888 "><i>  393   </i></font></a>          k_0_size_idx_1 = diagonal_size_idx_1;
<a name="394"><font color="#888888 "><i>  394   </i></font></a>          <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="395"><font color="#888888 "><i>  395   </i></font></a>            ixstart = (int32_T)index_data[iy];
<a name="396"><font color="#888888 "><i>  396   </i></font></a>            k_0_data[iy] = x_data[emlrtDynamicBoundsCheckFastR2012b(ixstart, 1,
<a name="397"><font color="#888888 "><i>  397   </i></font></a>              x_size[1], &amp;<a href="#var_j_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_j_emlrtBCI');" target="_self"><font color="#1122aa">j_emlrtBCI</font></a>, sp) - 1];
<a name="398"><font color="#888888 "><i>  398   </i></font></a>          <b>}</b>
<a name="399"><font color="#888888 "><i>  399   </i></font></a>        <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="400"><font color="#888888 "><i>  400   </i></font></a>          k_0_size_idx_1 = 1;
<a name="401"><font color="#888888 "><i>  401   </i></font></a>          iy = (int32_T)s;
<a name="402"><font color="#888888 "><i>  402   </i></font></a>          k_0_data[0] = initial_rates_data[emlrtDynamicBoundsCheckFastR2012b(iy,
<a name="403"><font color="#888888 "><i>  403   </i></font></a>            1, initial_rates_size[1], &amp;<a href="#var_i_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_i_emlrtBCI');" target="_self"><font color="#1122aa">i_emlrtBCI</font></a>, sp) - 1];
<a name="404"><font color="#888888 "><i>  404   </i></font></a>        <b>}</b>
<a name="405"><font color="#888888 "><i>  405   </i></font></a>
<a name="406"><font color="#888888 "><i>  406   </i></font></a>        st.site = &amp;<a href="#var_c_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_c_emlrtRSI');" target="_self"><font color="#1122aa">c_emlrtRSI</font></a>;
<a name="407"><font color="#888888 "><i>  407   </i></font></a>        alpha1 = s + N;
<a name="408"><font color="#888888 "><i>  408   </i></font></a>        ix = variables_indexes_size[0] * variables_indexes_size[1];
<a name="409"><font color="#888888 "><i>  409   </i></font></a>        <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="410"><font color="#888888 "><i>  410   </i></font></a>          b_x_data[iy] = (variables_indexes_data[iy] == alpha1);
<a name="411"><font color="#888888 "><i>  411   </i></font></a>        <b>}</b>
<a name="412"><font color="#888888 "><i>  412   </i></font></a>
<a name="413"><font color="#888888 "><i>  413   </i></font></a>        b_st.site = &amp;<a href="#var_g_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_g_emlrtRSI');" target="_self"><font color="#1122aa">g_emlrtRSI</font></a>;
<a name="414"><font color="#888888 "><i>  414   </i></font></a>        ixstart = 0;
<a name="415"><font color="#888888 "><i>  415   </i></font></a>        diagonal_size_idx_1 = variables_indexes_size[1];
<a name="416"><font color="#888888 "><i>  416   </i></font></a>        ix = 1;
<a name="417"><font color="#888888 "><i>  417   </i></font></a>        exitg2 = false;
<a name="418"><font color="#888888 "><i>  418   </i></font></a>        <font color="#112266"><b>while</b></font> ((!exitg2) &amp;&amp; (ix &lt;= variables_indexes_size[1])) <b>{</b>
<a name="419"><font color="#888888 "><i>  419   </i></font></a>          guard1 = false;
<a name="420"><font color="#888888 "><i>  420   </i></font></a>          <font color="#112266"><b>if</b></font> (b_x_data[ix - 1]) <b>{</b>
<a name="421"><font color="#888888 "><i>  421   </i></font></a>            ixstart++;
<a name="422"><font color="#888888 "><i>  422   </i></font></a>            ii_data[ixstart - 1] = ix;
<a name="423"><font color="#888888 "><i>  423   </i></font></a>            <font color="#112266"><b>if</b></font> (ixstart &gt;= variables_indexes_size[1]) <b>{</b>
<a name="424"><font color="#888888 "><i>  424   </i></font></a>              exitg2 = true;
<a name="425"><font color="#888888 "><i>  425   </i></font></a>            <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="426"><font color="#888888 "><i>  426   </i></font></a>              guard1 = true;
<a name="427"><font color="#888888 "><i>  427   </i></font></a>            <b>}</b>
<a name="428"><font color="#888888 "><i>  428   </i></font></a>          <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="429"><font color="#888888 "><i>  429   </i></font></a>            guard1 = true;
<a name="430"><font color="#888888 "><i>  430   </i></font></a>          <b>}</b>
<a name="431"><font color="#888888 "><i>  431   </i></font></a>
<a name="432"><font color="#888888 "><i>  432   </i></font></a>          <font color="#112266"><b>if</b></font> (guard1) <b>{</b>
<a name="433"><font color="#888888 "><i>  433   </i></font></a>            ix++;
<a name="434"><font color="#888888 "><i>  434   </i></font></a>          <b>}</b>
<a name="435"><font color="#888888 "><i>  435   </i></font></a>        <b>}</b>
<a name="436"><font color="#888888 "><i>  436   </i></font></a>
<a name="437"><font color="#888888 "><i>  437   </i></font></a>        <font color="#112266"><b>if</b></font> (ixstart &lt;= variables_indexes_size[1]) <b>{</b>
<a name="438"><font color="#888888 "><i>  438   </i></font></a>        <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="439"><font color="#888888 "><i>  439   </i></font></a>          b_y = NULL;
<a name="440"><font color="#888888 "><i>  440   </i></font></a>          m0 = emlrtCreateString(<font color="#1122ff">&quot;Assertion failed.&quot;</font>);
<a name="441"><font color="#888888 "><i>  441   </i></font></a>          emlrtAssign(&amp;b_y, m0);
<a name="442"><font color="#888888 "><i>  442   </i></font></a>          d_st.site = &amp;<a href="#var_n_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_n_emlrtRSI');" target="_self"><font color="#1122aa">n_emlrtRSI</font></a>;
<a name="443"><font color="#888888 "><i>  443   </i></font></a>          <a href="master_function_v4_mexutil_c.html#fcn_error" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_error');" target="_self"><font color="#1122aa">error</font></a>(&amp;d_st, b_y, &amp;<a href="#var_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtMCI');" target="_self"><font color="#1122aa">emlrtMCI</font></a>);
<a name="444"><font color="#888888 "><i>  444   </i></font></a>        <b>}</b>
<a name="445"><font color="#888888 "><i>  445   </i></font></a>
<a name="446"><font color="#888888 "><i>  446   </i></font></a>        <font color="#112266"><b>if</b></font> (variables_indexes_size[1] == 1) <b>{</b>
<a name="447"><font color="#888888 "><i>  447   </i></font></a>          <font color="#112266"><b>if</b></font> (ixstart == 0) <b>{</b>
<a name="448"><font color="#888888 "><i>  448   </i></font></a>            diagonal_size_idx_1 = 0;
<a name="449"><font color="#888888 "><i>  449   </i></font></a>          <b>}</b>
<a name="450"><font color="#888888 "><i>  450   </i></font></a>        <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="451"><font color="#888888 "><i>  451   </i></font></a>          <font color="#112266"><b>if</b></font> (1 &gt; ixstart) <b>{</b>
<a name="452"><font color="#888888 "><i>  452   </i></font></a>            diagonal_size_idx_1 = 0;
<a name="453"><font color="#888888 "><i>  453   </i></font></a>          <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="454"><font color="#888888 "><i>  454   </i></font></a>            diagonal_size_idx_1 = ixstart;
<a name="455"><font color="#888888 "><i>  455   </i></font></a>          <b>}</b>
<a name="456"><font color="#888888 "><i>  456   </i></font></a>
<a name="457"><font color="#888888 "><i>  457   </i></font></a>          <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="458"><font color="#888888 "><i>  458   </i></font></a>            b_ii_data[iy] = ii_data[iy];
<a name="459"><font color="#888888 "><i>  459   </i></font></a>          <b>}</b>
<a name="460"><font color="#888888 "><i>  460   </i></font></a>
<a name="461"><font color="#888888 "><i>  461   </i></font></a>          <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="462"><font color="#888888 "><i>  462   </i></font></a>            ii_data[iy] = b_ii_data[iy];
<a name="463"><font color="#888888 "><i>  463   </i></font></a>          <b>}</b>
<a name="464"><font color="#888888 "><i>  464   </i></font></a>        <b>}</b>
<a name="465"><font color="#888888 "><i>  465   </i></font></a>
<a name="466"><font color="#888888 "><i>  466   </i></font></a>        index_size[0] = 1;
<a name="467"><font color="#888888 "><i>  467   </i></font></a>        index_size[1] = diagonal_size_idx_1;
<a name="468"><font color="#888888 "><i>  468   </i></font></a>        ix = diagonal_size_idx_1;
<a name="469"><font color="#888888 "><i>  469   </i></font></a>        <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="470"><font color="#888888 "><i>  470   </i></font></a>          index_data[iy] = ii_data[iy];
<a name="471"><font color="#888888 "><i>  471   </i></font></a>        <b>}</b>
<a name="472"><font color="#888888 "><i>  472   </i></font></a>
<a name="473"><font color="#888888 "><i>  473   </i></font></a>        st.site = &amp;<a href="#var_d_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_d_emlrtRSI');" target="_self"><font color="#1122aa">d_emlrtRSI</font></a>;
<a name="474"><font color="#888888 "><i>  474   </i></font></a>        <font color="#112266"><b>if</b></font> (<a href="sum_c.html#fcn_sum" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_sum');" target="_self"><font color="#1122aa">sum</font></a>(&amp;st, index_data, index_size) &gt; 0.0) <b>{</b>
<a name="475"><font color="#888888 "><i>  475   </i></font></a>          <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="476"><font color="#888888 "><i>  476   </i></font></a>            ixstart = (int32_T)index_data[iy];
<a name="477"><font color="#888888 "><i>  477   </i></font></a>            x_0_data[iy] = x_data[emlrtDynamicBoundsCheckFastR2012b(ixstart, 1,
<a name="478"><font color="#888888 "><i>  478   </i></font></a>              x_size[1], &amp;<a href="#var_l_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_l_emlrtBCI');" target="_self"><font color="#1122aa">l_emlrtBCI</font></a>, sp) - 1];
<a name="479"><font color="#888888 "><i>  479   </i></font></a>          <b>}</b>
<a name="480"><font color="#888888 "><i>  480   </i></font></a>        <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="481"><font color="#888888 "><i>  481   </i></font></a>          diagonal_size_idx_1 = 1;
<a name="482"><font color="#888888 "><i>  482   </i></font></a>          alpha1 = s + N;
<a name="483"><font color="#888888 "><i>  483   </i></font></a>          iy = (int32_T)emlrtIntegerCheckFastR2012b(alpha1, &amp;<a href="#var_emlrtDCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtDCI');" target="_self"><font color="#1122aa">emlrtDCI</font></a>, sp);
<a name="484"><font color="#888888 "><i>  484   </i></font></a>          x_0_data[0] = initial_rates_data[emlrtDynamicBoundsCheckFastR2012b(iy,
<a name="485"><font color="#888888 "><i>  485   </i></font></a>            1, initial_rates_size[1], &amp;<a href="#var_k_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_k_emlrtBCI');" target="_self"><font color="#1122aa">k_emlrtBCI</font></a>, sp) - 1];
<a name="486"><font color="#888888 "><i>  486   </i></font></a>        <b>}</b>
<a name="487"><font color="#888888 "><i>  487   </i></font></a>
<a name="488"><font color="#888888 "><i>  488   </i></font></a>        <font color="#117755"><i>/* x_0 */</i></font>
<a name="489"><font color="#888888 "><i>  489   </i></font></a>        emlrtDynamicBoundsCheckFastR2012b(1, 1, k_0_size_idx_1, &amp;<a href="#var_c_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_c_emlrtBCI');" target="_self"><font color="#1122aa">c_emlrtBCI</font></a>, sp);
<a name="490"><font color="#888888 "><i>  490   </i></font></a>        emlrtDynamicBoundsCheckFastR2012b(1, 1, diagonal_size_idx_1, &amp;<a href="#var_b_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_b_emlrtBCI');" target="_self"><font color="#1122aa">b_emlrtBCI</font></a>,
<a name="491"><font color="#888888 "><i>  491   </i></font></a>          sp);
<a name="492"><font color="#888888 "><i>  492   </i></font></a>        rate_matrix_data[(emlrtDynamicBoundsCheckFastR2012b(i, 1,
<a name="493"><font color="#888888 "><i>  493   </i></font></a>          transitions_matrix_size[0], &amp;<a href="#var_m_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_m_emlrtBCI');" target="_self"><font color="#1122aa">m_emlrtBCI</font></a>, sp) +
<a name="494"><font color="#888888 "><i>  494   </i></font></a>                          transitions_matrix_size[0] *
<a name="495"><font color="#888888 "><i>  495   </i></font></a>                          (emlrtDynamicBoundsCheckFastR2012b(j, 1,
<a name="496"><font color="#888888 "><i>  496   </i></font></a>          transitions_matrix_size[1], &amp;<a href="#var_n_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_n_emlrtBCI');" target="_self"><font color="#1122aa">n_emlrtBCI</font></a>, sp) - 1)) - 1] = k_0_data[0] *
<a name="497"><font color="#888888 "><i>  497   </i></font></a>          muDoubleScalarExp(t * force_rate * x_0_data[0] / 4.1);
<a name="498"><font color="#888888 "><i>  498   </i></font></a>        <font color="#112266"><b>if</b></font> (rate_matrix_data[(emlrtDynamicBoundsCheckFastR2012b(i, 1,
<a name="499"><font color="#888888 "><i>  499   </i></font></a>              transitions_matrix_size[0], &amp;<a href="#var_o_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_o_emlrtBCI');" target="_self"><font color="#1122aa">o_emlrtBCI</font></a>, sp) +
<a name="500"><font color="#888888 "><i>  500   </i></font></a>                              transitions_matrix_size[0] *
<a name="501"><font color="#888888 "><i>  501   </i></font></a>                              (emlrtDynamicBoundsCheckFastR2012b(j, 1,
<a name="502"><font color="#888888 "><i>  502   </i></font></a>               transitions_matrix_size[1], &amp;<a href="#var_p_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_p_emlrtBCI');" target="_self"><font color="#1122aa">p_emlrtBCI</font></a>, sp) - 1)) - 1] &gt;= 5000.0)
<a name="503"><font color="#888888 "><i>  503   </i></font></a>        <b>{</b>
<a name="504"><font color="#888888 "><i>  504   </i></font></a>          rate_matrix_data[(emlrtDynamicBoundsCheckFastR2012b(i, 1,
<a name="505"><font color="#888888 "><i>  505   </i></font></a>            transitions_matrix_size[0], &amp;<a href="#var_q_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_q_emlrtBCI');" target="_self"><font color="#1122aa">q_emlrtBCI</font></a>, sp) +
<a name="506"><font color="#888888 "><i>  506   </i></font></a>                            transitions_matrix_size[0] *
<a name="507"><font color="#888888 "><i>  507   </i></font></a>                            (emlrtDynamicBoundsCheckFastR2012b(j, 1,
<a name="508"><font color="#888888 "><i>  508   </i></font></a>            transitions_matrix_size[1], &amp;<a href="#var_r_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_r_emlrtBCI');" target="_self"><font color="#1122aa">r_emlrtBCI</font></a>, sp) - 1)) - 1] = 5000.0;
<a name="509"><font color="#888888 "><i>  509   </i></font></a>        <b>}</b>
<a name="510"><font color="#888888 "><i>  510   </i></font></a>
<a name="511"><font color="#888888 "><i>  511   </i></font></a>        s++;
<a name="512"><font color="#888888 "><i>  512   </i></font></a>      <b>}</b>
<a name="513"><font color="#888888 "><i>  513   </i></font></a>
<a name="514"><font color="#888888 "><i>  514   </i></font></a>      j++;
<a name="515"><font color="#888888 "><i>  515   </i></font></a>      emlrtBreakCheckFastR2012b(<a href="master_function_v4_data_c.html#var_emlrtBreakCheckR2012bFlagVar" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtBreakCheckR2012bFlagVar');" target="_self"><font color="#1122aa">emlrtBreakCheckR2012bFlagVar</font></a>, sp);
<a name="516"><font color="#888888 "><i>  516   </i></font></a>    <b>}</b>
<a name="517"><font color="#888888 "><i>  517   </i></font></a>
<a name="518"><font color="#888888 "><i>  518   </i></font></a>    i++;
<a name="519"><font color="#888888 "><i>  519   </i></font></a>    emlrtBreakCheckFastR2012b(<a href="master_function_v4_data_c.html#var_emlrtBreakCheckR2012bFlagVar" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtBreakCheckR2012bFlagVar');" target="_self"><font color="#1122aa">emlrtBreakCheckR2012bFlagVar</font></a>, sp);
<a name="520"><font color="#888888 "><i>  520   </i></font></a>  <b>}</b>
<a name="521"><font color="#888888 "><i>  521   </i></font></a>
<a name="522"><font color="#888888 "><i>  522   </i></font></a>  st.site = &amp;<a href="#var_e_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_e_emlrtRSI');" target="_self"><font color="#1122aa">e_emlrtRSI</font></a>;
<a name="523"><font color="#888888 "><i>  523   </i></font></a>  p = false;
<a name="524"><font color="#888888 "><i>  524   </i></font></a>  b_p = false;
<a name="525"><font color="#888888 "><i>  525   </i></font></a>  ixstart = 0;
<a name="526"><font color="#888888 "><i>  526   </i></font></a>  <font color="#112266"><b>do</b></font> <b>{</b>
<a name="527"><font color="#888888 "><i>  527   </i></font></a>    exitg1 = 0;
<a name="528"><font color="#888888 "><i>  528   </i></font></a>    <font color="#112266"><b>if</b></font> (ixstart &lt; 2) <b>{</b>
<a name="529"><font color="#888888 "><i>  529   </i></font></a>      <font color="#112266"><b>if</b></font> (rate_matrix_size[ixstart] != 0) <b>{</b>
<a name="530"><font color="#888888 "><i>  530   </i></font></a>        exitg1 = 1;
<a name="531"><font color="#888888 "><i>  531   </i></font></a>      <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="532"><font color="#888888 "><i>  532   </i></font></a>        ixstart++;
<a name="533"><font color="#888888 "><i>  533   </i></font></a>      <b>}</b>
<a name="534"><font color="#888888 "><i>  534   </i></font></a>    <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="535"><font color="#888888 "><i>  535   </i></font></a>      b_p = true;
<a name="536"><font color="#888888 "><i>  536   </i></font></a>      exitg1 = 1;
<a name="537"><font color="#888888 "><i>  537   </i></font></a>    <b>}</b>
<a name="538"><font color="#888888 "><i>  538   </i></font></a>  <b>}</b> <font color="#112266"><b>while</b></font> (exitg1 == 0);
<a name="539"><font color="#888888 "><i>  539   </i></font></a>
<a name="540"><font color="#888888 "><i>  540   </i></font></a>  <font color="#112266"><b>if</b></font> (!b_p) <b>{</b>
<a name="541"><font color="#888888 "><i>  541   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="542"><font color="#888888 "><i>  542   </i></font></a>    p = true;
<a name="543"><font color="#888888 "><i>  543   </i></font></a>  <b>}</b>
<a name="544"><font color="#888888 "><i>  544   </i></font></a>
<a name="545"><font color="#888888 "><i>  545   </i></font></a>  <font color="#112266"><b>if</b></font> (!p) <b>{</b>
<a name="546"><font color="#888888 "><i>  546   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="547"><font color="#888888 "><i>  547   </i></font></a>    c_y = NULL;
<a name="548"><font color="#888888 "><i>  548   </i></font></a>    m0 = emlrtCreateCharArray(2, iv0);
<a name="549"><font color="#888888 "><i>  549   </i></font></a>    <font color="#112266"><b>for</b></font> (i = 0; i &lt; 30; i++) <b>{</b>
<a name="550"><font color="#888888 "><i>  550   </i></font></a>      cv0[i] = cv1[i];
<a name="551"><font color="#888888 "><i>  551   </i></font></a>    <b>}</b>
<a name="552"><font color="#888888 "><i>  552   </i></font></a>
<a name="553"><font color="#888888 "><i>  553   </i></font></a>    emlrtInitCharArrayR2013a(&amp;st, 30, m0, cv0);
<a name="554"><font color="#888888 "><i>  554   </i></font></a>    emlrtAssign(&amp;c_y, m0);
<a name="555"><font color="#888888 "><i>  555   </i></font></a>    b_st.site = &amp;<a href="master_function_v4_data_c.html#var_m_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_m_emlrtRSI');" target="_self"><font color="#1122aa">m_emlrtRSI</font></a>;
<a name="556"><font color="#888888 "><i>  556   </i></font></a>    c_st.site = &amp;<a href="master_function_v4_data_c.html#var_r_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_r_emlrtRSI');" target="_self"><font color="#1122aa">r_emlrtRSI</font></a>;
<a name="557"><font color="#888888 "><i>  557   </i></font></a>    <a href="master_function_v4_mexutil_c.html#fcn_error" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_error');" target="_self"><font color="#1122aa">error</font></a>(&amp;b_st, <a href="master_function_v4_mexutil_c.html#fcn_message" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_message');" target="_self"><font color="#1122aa">message</font></a>(&amp;c_st, c_y, &amp;<a href="master_function_v4_data_c.html#var_b_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_b_emlrtMCI');" target="_self"><font color="#1122aa">b_emlrtMCI</font></a>), &amp;<a href="master_function_v4_data_c.html#var_c_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_c_emlrtMCI');" target="_self"><font color="#1122aa">c_emlrtMCI</font></a>);
<a name="558"><font color="#888888 "><i>  558   </i></font></a>  <b>}</b>
<a name="559"><font color="#888888 "><i>  559   </i></font></a>
<a name="560"><font color="#888888 "><i>  560   </i></font></a>  <font color="#112266"><b>if</b></font> (((transitions_matrix_size[0] == 1) &amp;&amp; (transitions_matrix_size[1] == 1)) ||
<a name="561"><font color="#888888 "><i>  561   </i></font></a>      (transitions_matrix_size[0] != 1)) <b>{</b>
<a name="562"><font color="#888888 "><i>  562   </i></font></a>    p = true;
<a name="563"><font color="#888888 "><i>  563   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="564"><font color="#888888 "><i>  564   </i></font></a>    p = false;
<a name="565"><font color="#888888 "><i>  565   </i></font></a>  <b>}</b>
<a name="566"><font color="#888888 "><i>  566   </i></font></a>
<a name="567"><font color="#888888 "><i>  567   </i></font></a>  <font color="#112266"><b>if</b></font> (p) <b>{</b>
<a name="568"><font color="#888888 "><i>  568   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="569"><font color="#888888 "><i>  569   </i></font></a>    d_y = NULL;
<a name="570"><font color="#888888 "><i>  570   </i></font></a>    m0 = emlrtCreateCharArray(2, iv1);
<a name="571"><font color="#888888 "><i>  571   </i></font></a>    <font color="#112266"><b>for</b></font> (i = 0; i &lt; 36; i++) <b>{</b>
<a name="572"><font color="#888888 "><i>  572   </i></font></a>      cv2[i] = cv3[i];
<a name="573"><font color="#888888 "><i>  573   </i></font></a>    <b>}</b>
<a name="574"><font color="#888888 "><i>  574   </i></font></a>
<a name="575"><font color="#888888 "><i>  575   </i></font></a>    emlrtInitCharArrayR2013a(&amp;st, 36, m0, cv2);
<a name="576"><font color="#888888 "><i>  576   </i></font></a>    emlrtAssign(&amp;d_y, m0);
<a name="577"><font color="#888888 "><i>  577   </i></font></a>    b_st.site = &amp;<a href="master_function_v4_data_c.html#var_l_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_l_emlrtRSI');" target="_self"><font color="#1122aa">l_emlrtRSI</font></a>;
<a name="578"><font color="#888888 "><i>  578   </i></font></a>    c_st.site = &amp;<a href="master_function_v4_data_c.html#var_q_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_q_emlrtRSI');" target="_self"><font color="#1122aa">q_emlrtRSI</font></a>;
<a name="579"><font color="#888888 "><i>  579   </i></font></a>    <a href="master_function_v4_mexutil_c.html#fcn_error" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_error');" target="_self"><font color="#1122aa">error</font></a>(&amp;b_st, <a href="master_function_v4_mexutil_c.html#fcn_message" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_message');" target="_self"><font color="#1122aa">message</font></a>(&amp;c_st, d_y, &amp;<a href="master_function_v4_data_c.html#var_d_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_d_emlrtMCI');" target="_self"><font color="#1122aa">d_emlrtMCI</font></a>), &amp;<a href="master_function_v4_data_c.html#var_e_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_e_emlrtMCI');" target="_self"><font color="#1122aa">e_emlrtMCI</font></a>);
<a name="580"><font color="#888888 "><i>  580   </i></font></a>  <b>}</b>
<a name="581"><font color="#888888 "><i>  581   </i></font></a>
<a name="582"><font color="#888888 "><i>  582   </i></font></a>  <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; 2; iy++) <b>{</b>
<a name="583"><font color="#888888 "><i>  583   </i></font></a>    sz[iy] = (int8_T)rate_matrix_size[iy];
<a name="584"><font color="#888888 "><i>  584   </i></font></a>  <b>}</b>
<a name="585"><font color="#888888 "><i>  585   </i></font></a>
<a name="586"><font color="#888888 "><i>  586   </i></font></a>  diagonal_size_idx_1 = sz[1];
<a name="587"><font color="#888888 "><i>  587   </i></font></a>  <font color="#112266"><b>if</b></font> ((transitions_matrix_size[0] == 0) || (transitions_matrix_size[1] == 0)) <b>{</b>
<a name="588"><font color="#888888 "><i>  588   </i></font></a>    diagonal_size_idx_1 = sz[1];
<a name="589"><font color="#888888 "><i>  589   </i></font></a>    ix = sz[1];
<a name="590"><font color="#888888 "><i>  590   </i></font></a>    <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="591"><font color="#888888 "><i>  591   </i></font></a>      diagonal_data[iy] = 0.0;
<a name="592"><font color="#888888 "><i>  592   </i></font></a>    <b>}</b>
<a name="593"><font color="#888888 "><i>  593   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="594"><font color="#888888 "><i>  594   </i></font></a>    ix = -1;
<a name="595"><font color="#888888 "><i>  595   </i></font></a>    iy = -1;
<a name="596"><font color="#888888 "><i>  596   </i></font></a>    <font color="#112266"><b>for</b></font> (i = 1; i &lt;= transitions_matrix_size[1]; i++) <b>{</b>
<a name="597"><font color="#888888 "><i>  597   </i></font></a>      ixstart = ix + 1;
<a name="598"><font color="#888888 "><i>  598   </i></font></a>      ix++;
<a name="599"><font color="#888888 "><i>  599   </i></font></a>      s = rate_matrix_data[ixstart];
<a name="600"><font color="#888888 "><i>  600   </i></font></a>      <font color="#112266"><b>for</b></font> (ixstart = 2; ixstart &lt;= transitions_matrix_size[0]; ixstart++) <b>{</b>
<a name="601"><font color="#888888 "><i>  601   </i></font></a>        ix++;
<a name="602"><font color="#888888 "><i>  602   </i></font></a>        s += rate_matrix_data[ix];
<a name="603"><font color="#888888 "><i>  603   </i></font></a>      <b>}</b>
<a name="604"><font color="#888888 "><i>  604   </i></font></a>
<a name="605"><font color="#888888 "><i>  605   </i></font></a>      iy++;
<a name="606"><font color="#888888 "><i>  606   </i></font></a>      diagonal_data[iy] = s;
<a name="607"><font color="#888888 "><i>  607   </i></font></a>    <b>}</b>
<a name="608"><font color="#888888 "><i>  608   </i></font></a>  <b>}</b>
<a name="609"><font color="#888888 "><i>  609   </i></font></a>
<a name="610"><font color="#888888 "><i>  610   </i></font></a>  <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; diagonal_size_idx_1; iy++) <b>{</b>
<a name="611"><font color="#888888 "><i>  611   </i></font></a>    diagonal_data[iy] = -diagonal_data[iy];
<a name="612"><font color="#888888 "><i>  612   </i></font></a>  <b>}</b>
<a name="613"><font color="#888888 "><i>  613   </i></font></a>
<a name="614"><font color="#888888 "><i>  614   </i></font></a>  <font color="#112266"><b>if</b></font> ((0 == transitions_matrix_size[0]) || (0 == transitions_matrix_size[1])) <b>{</b>
<a name="615"><font color="#888888 "><i>  615   </i></font></a>    n = 0;
<a name="616"><font color="#888888 "><i>  616   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="617"><font color="#888888 "><i>  617   </i></font></a>    n = muIntScalarMax_sint32(transitions_matrix_size[0],
<a name="618"><font color="#888888 "><i>  618   </i></font></a>      transitions_matrix_size[1]);
<a name="619"><font color="#888888 "><i>  619   </i></font></a>  <b>}</b>
<a name="620"><font color="#888888 "><i>  620   </i></font></a>
<a name="621"><font color="#888888 "><i>  621   </i></font></a>  i = 1;
<a name="622"><font color="#888888 "><i>  622   </i></font></a>  <font color="#112266"><b>while</b></font> (i - 1 &lt;= n - 1) <b>{</b>
<a name="623"><font color="#888888 "><i>  623   </i></font></a>    rate_matrix_data[(emlrtDynamicBoundsCheckFastR2012b(i, 1,
<a name="624"><font color="#888888 "><i>  624   </i></font></a>      transitions_matrix_size[0], &amp;<a href="#var_d_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_d_emlrtBCI');" target="_self"><font color="#1122aa">d_emlrtBCI</font></a>, sp) + transitions_matrix_size[0] *
<a name="625"><font color="#888888 "><i>  625   </i></font></a>                      (emlrtDynamicBoundsCheckFastR2012b(i, 1,
<a name="626"><font color="#888888 "><i>  626   </i></font></a>      transitions_matrix_size[1], &amp;<a href="#var_e_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_e_emlrtBCI');" target="_self"><font color="#1122aa">e_emlrtBCI</font></a>, sp) - 1)) - 1] =
<a name="627"><font color="#888888 "><i>  627   </i></font></a>      diagonal_data[emlrtDynamicBoundsCheckFastR2012b(i, 1, diagonal_size_idx_1,
<a name="628"><font color="#888888 "><i>  628   </i></font></a>      &amp;<a href="#var_f_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_f_emlrtBCI');" target="_self"><font color="#1122aa">f_emlrtBCI</font></a>, sp) - 1];
<a name="629"><font color="#888888 "><i>  629   </i></font></a>    i++;
<a name="630"><font color="#888888 "><i>  630   </i></font></a>    emlrtBreakCheckFastR2012b(<a href="master_function_v4_data_c.html#var_emlrtBreakCheckR2012bFlagVar" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtBreakCheckR2012bFlagVar');" target="_self"><font color="#1122aa">emlrtBreakCheckR2012bFlagVar</font></a>, sp);
<a name="631"><font color="#888888 "><i>  631   </i></font></a>  <b>}</b>
<a name="632"><font color="#888888 "><i>  632   </i></font></a>
<a name="633"><font color="#888888 "><i>  633   </i></font></a>  st.site = &amp;<a href="#var_f_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_f_emlrtRSI');" target="_self"><font color="#1122aa">f_emlrtRSI</font></a>;
<a name="634"><font color="#888888 "><i>  634   </i></font></a>  b_st.site = &amp;<a href="#var_i_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_i_emlrtRSI');" target="_self"><font color="#1122aa">i_emlrtRSI</font></a>;
<a name="635"><font color="#888888 "><i>  635   </i></font></a>  <font color="#112266"><b>if</b></font> (!(transitions_matrix_size[1] == y_size[0])) <b>{</b>
<a name="636"><font color="#888888 "><i>  636   </i></font></a>    <font color="#112266"><b>if</b></font> (((transitions_matrix_size[0] == 1) &amp;&amp; (transitions_matrix_size[1] == 1))
<a name="637"><font color="#888888 "><i>  637   </i></font></a>        || (y_size[0] == 1)) <b>{</b>
<a name="638"><font color="#888888 "><i>  638   </i></font></a>      e_y = NULL;
<a name="639"><font color="#888888 "><i>  639   </i></font></a>      m0 = emlrtCreateCharArray(2, iv2);
<a name="640"><font color="#888888 "><i>  640   </i></font></a>      <font color="#112266"><b>for</b></font> (i = 0; i &lt; 45; i++) <b>{</b>
<a name="641"><font color="#888888 "><i>  641   </i></font></a>        cv4[i] = cv5[i];
<a name="642"><font color="#888888 "><i>  642   </i></font></a>      <b>}</b>
<a name="643"><font color="#888888 "><i>  643   </i></font></a>
<a name="644"><font color="#888888 "><i>  644   </i></font></a>      emlrtInitCharArrayR2013a(&amp;b_st, 45, m0, cv4);
<a name="645"><font color="#888888 "><i>  645   </i></font></a>      emlrtAssign(&amp;e_y, m0);
<a name="646"><font color="#888888 "><i>  646   </i></font></a>      d_st.site = &amp;<a href="#var_o_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_o_emlrtRSI');" target="_self"><font color="#1122aa">o_emlrtRSI</font></a>;
<a name="647"><font color="#888888 "><i>  647   </i></font></a>      e_st.site = &amp;<a href="#var_s_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_s_emlrtRSI');" target="_self"><font color="#1122aa">s_emlrtRSI</font></a>;
<a name="648"><font color="#888888 "><i>  648   </i></font></a>      <a href="master_function_v4_mexutil_c.html#fcn_error" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_error');" target="_self"><font color="#1122aa">error</font></a>(&amp;d_st, <a href="master_function_v4_mexutil_c.html#fcn_message" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_message');" target="_self"><font color="#1122aa">message</font></a>(&amp;e_st, e_y, &amp;<a href="#var_f_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_f_emlrtMCI');" target="_self"><font color="#1122aa">f_emlrtMCI</font></a>), &amp;<a href="#var_g_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_g_emlrtMCI');" target="_self"><font color="#1122aa">g_emlrtMCI</font></a>);
<a name="649"><font color="#888888 "><i>  649   </i></font></a>    <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="650"><font color="#888888 "><i>  650   </i></font></a>      f_y = NULL;
<a name="651"><font color="#888888 "><i>  651   </i></font></a>      m0 = emlrtCreateCharArray(2, iv3);
<a name="652"><font color="#888888 "><i>  652   </i></font></a>      <font color="#112266"><b>for</b></font> (i = 0; i &lt; 21; i++) <b>{</b>
<a name="653"><font color="#888888 "><i>  653   </i></font></a>        cv6[i] = cv7[i];
<a name="654"><font color="#888888 "><i>  654   </i></font></a>      <b>}</b>
<a name="655"><font color="#888888 "><i>  655   </i></font></a>
<a name="656"><font color="#888888 "><i>  656   </i></font></a>      emlrtInitCharArrayR2013a(&amp;b_st, 21, m0, cv6);
<a name="657"><font color="#888888 "><i>  657   </i></font></a>      emlrtAssign(&amp;f_y, m0);
<a name="658"><font color="#888888 "><i>  658   </i></font></a>      d_st.site = &amp;<a href="#var_p_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_p_emlrtRSI');" target="_self"><font color="#1122aa">p_emlrtRSI</font></a>;
<a name="659"><font color="#888888 "><i>  659   </i></font></a>      e_st.site = &amp;<a href="#var_t_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_t_emlrtRSI');" target="_self"><font color="#1122aa">t_emlrtRSI</font></a>;
<a name="660"><font color="#888888 "><i>  660   </i></font></a>      <a href="master_function_v4_mexutil_c.html#fcn_error" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_error');" target="_self"><font color="#1122aa">error</font></a>(&amp;d_st, <a href="master_function_v4_mexutil_c.html#fcn_message" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'fcn_message');" target="_self"><font color="#1122aa">message</font></a>(&amp;e_st, f_y, &amp;<a href="#var_h_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_h_emlrtMCI');" target="_self"><font color="#1122aa">h_emlrtMCI</font></a>), &amp;<a href="#var_i_emlrtMCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_i_emlrtMCI');" target="_self"><font color="#1122aa">i_emlrtMCI</font></a>);
<a name="661"><font color="#888888 "><i>  661   </i></font></a>    <b>}</b>
<a name="662"><font color="#888888 "><i>  662   </i></font></a>  <b>}</b>
<a name="663"><font color="#888888 "><i>  663   </i></font></a>
<a name="664"><font color="#888888 "><i>  664   </i></font></a>  <font color="#112266"><b>if</b></font> ((transitions_matrix_size[1] == 1) || (y_size[0] == 1)) <b>{</b>
<a name="665"><font color="#888888 "><i>  665   </i></font></a>    dy_size[0] = transitions_matrix_size[0];
<a name="666"><font color="#888888 "><i>  666   </i></font></a>    ix = transitions_matrix_size[0];
<a name="667"><font color="#888888 "><i>  667   </i></font></a>    <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="668"><font color="#888888 "><i>  668   </i></font></a>      dy_data[iy] = 0.0;
<a name="669"><font color="#888888 "><i>  669   </i></font></a>      diagonal_size_idx_1 = transitions_matrix_size[1];
<a name="670"><font color="#888888 "><i>  670   </i></font></a>      <font color="#112266"><b>for</b></font> (ixstart = 0; ixstart &lt; diagonal_size_idx_1; ixstart++) <b>{</b>
<a name="671"><font color="#888888 "><i>  671   </i></font></a>        dy_data[iy] += rate_matrix_data[iy + transitions_matrix_size[0] *
<a name="672"><font color="#888888 "><i>  672   </i></font></a>          ixstart] * y_data[ixstart];
<a name="673"><font color="#888888 "><i>  673   </i></font></a>      <b>}</b>
<a name="674"><font color="#888888 "><i>  674   </i></font></a>    <b>}</b>
<a name="675"><font color="#888888 "><i>  675   </i></font></a>  <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="676"><font color="#888888 "><i>  676   </i></font></a>    b_st.site = &amp;<a href="#var_h_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_h_emlrtRSI');" target="_self"><font color="#1122aa">h_emlrtRSI</font></a>;
<a name="677"><font color="#888888 "><i>  677   </i></font></a>    d_st.site = &amp;<a href="#var_j_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_j_emlrtRSI');" target="_self"><font color="#1122aa">j_emlrtRSI</font></a>;
<a name="678"><font color="#888888 "><i>  678   </i></font></a>    dy_size[0] = (int8_T)transitions_matrix_size[0];
<a name="679"><font color="#888888 "><i>  679   </i></font></a>    ix = (int8_T)transitions_matrix_size[0];
<a name="680"><font color="#888888 "><i>  680   </i></font></a>    <font color="#112266"><b>for</b></font> (iy = 0; iy &lt; ix; iy++) <b>{</b>
<a name="681"><font color="#888888 "><i>  681   </i></font></a>      dy_data[iy] = 0.0;
<a name="682"><font color="#888888 "><i>  682   </i></font></a>    <b>}</b>
<a name="683"><font color="#888888 "><i>  683   </i></font></a>
<a name="684"><font color="#888888 "><i>  684   </i></font></a>    <font color="#112266"><b>if</b></font> ((transitions_matrix_size[0] &lt; 1) || (transitions_matrix_size[1] &lt; 1)) <b>{</b>
<a name="685"><font color="#888888 "><i>  685   </i></font></a>    <b>}</b> <font color="#112266"><b>else</b></font> <b>{</b>
<a name="686"><font color="#888888 "><i>  686   </i></font></a>      f_st.site = &amp;<a href="#var_k_emlrtRSI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_k_emlrtRSI');" target="_self"><font color="#1122aa">k_emlrtRSI</font></a>;
<a name="687"><font color="#888888 "><i>  687   </i></font></a>      alpha1 = 1.0;
<a name="688"><font color="#888888 "><i>  688   </i></font></a>      s = 0.0;
<a name="689"><font color="#888888 "><i>  689   </i></font></a>      TRANSB = <font color="#1122ff">'N'</font>;
<a name="690"><font color="#888888 "><i>  690   </i></font></a>      TRANSA = <font color="#1122ff">'N'</font>;
<a name="691"><font color="#888888 "><i>  691   </i></font></a>      m_t = (ptrdiff_t)(transitions_matrix_size[0]);
<a name="692"><font color="#888888 "><i>  692   </i></font></a>      n_t = (ptrdiff_t)(1);
<a name="693"><font color="#888888 "><i>  693   </i></font></a>      k_t = (ptrdiff_t)(transitions_matrix_size[1]);
<a name="694"><font color="#888888 "><i>  694   </i></font></a>      lda_t = (ptrdiff_t)(transitions_matrix_size[0]);
<a name="695"><font color="#888888 "><i>  695   </i></font></a>      ldb_t = (ptrdiff_t)(transitions_matrix_size[1]);
<a name="696"><font color="#888888 "><i>  696   </i></font></a>      ldc_t = (ptrdiff_t)(transitions_matrix_size[0]);
<a name="697"><font color="#888888 "><i>  697   </i></font></a>      alpha1_t = (<font color="#112266"><b>double</b></font> *)(&amp;alpha1);
<a name="698"><font color="#888888 "><i>  698   </i></font></a>      Aia0_t = (<font color="#112266"><b>double</b></font> *)(&amp;rate_matrix_data[0]);
<a name="699"><font color="#888888 "><i>  699   </i></font></a>      emlrtDynamicBoundsCheckFastR2012b(1, 1, y_size[0], &amp;<a href="#var_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtBCI');" target="_self"><font color="#1122aa">emlrtBCI</font></a>, &amp;f_st);
<a name="700"><font color="#888888 "><i>  700   </i></font></a>      Bib0_t = (<font color="#112266"><b>double</b></font> *)(&amp;y_data[0]);
<a name="701"><font color="#888888 "><i>  701   </i></font></a>      beta1_t = (<font color="#112266"><b>double</b></font> *)(&amp;s);
<a name="702"><font color="#888888 "><i>  702   </i></font></a>      iy = (int8_T)transitions_matrix_size[0];
<a name="703"><font color="#888888 "><i>  703   </i></font></a>      emlrtDynamicBoundsCheckFastR2012b(1, 1, iy, &amp;<a href="#var_emlrtBCI" onclick="if (top) if (top.docHiliteMe) top.docHiliteMe(window, 'var_emlrtBCI');" target="_self"><font color="#1122aa">emlrtBCI</font></a>, &amp;f_st);
<a name="704"><font color="#888888 "><i>  704   </i></font></a>      Cic0_t = (<font color="#112266"><b>double</b></font> *)(&amp;dy_data[0]);
<a name="705"><font color="#888888 "><i>  705   </i></font></a>      dgemm(&amp;TRANSA, &amp;TRANSB, &amp;m_t, &amp;n_t, &amp;k_t, alpha1_t, Aia0_t, &amp;lda_t, Bib0_t,
<a name="706"><font color="#888888 "><i>  706   </i></font></a>            &amp;ldb_t, beta1_t, Cic0_t, &amp;ldc_t);
<a name="707"><font color="#888888 "><i>  707   </i></font></a>    <b>}</b>
<a name="708"><font color="#888888 "><i>  708   </i></font></a>  <b>}</b>
<a name="709"><font color="#888888 "><i>  709   </i></font></a><b>}</b>
<a name="710"><font color="#888888 "><i>  710   </i></font></a>
<a name="711"><font color="#888888 "><i>  711   </i></font></a><font color="#117755"><i>/* End of code generation (master_function_v4.c) */</i></font>
<a name="712"><font color="#888888 "><i>  712   </i></font></a></pre>
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